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Polycomb protein Scm (Sex comb on midleg protein)

 SCM_DROME               Reviewed;         877 AA.
Q9VHA0; Q24191;
01-MAR-2005, integrated into UniProtKB/Swiss-Prot.
01-OCT-2002, sequence version 2.
25-OCT-2017, entry version 154.
RecName: Full=Polycomb protein Scm;
AltName: Full=Sex comb on midleg protein;
Name=Scm {ECO:0000312|EMBL:AAF54419.2}; ORFNames=CG9495;
Drosophila melanogaster (Fruit fly).
Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta;
Pterygota; Neoptera; Holometabola; Diptera; Brachycera; Muscomorpha;
Ephydroidea; Drosophilidae; Drosophila; Sophophora.
NCBI_TaxID=7227;
[1] {ECO:0000305, ECO:0000312|EMBL:AAB57632.1}
NUCLEOTIDE SEQUENCE [MRNA], AND DEVELOPMENTAL STAGE.
TISSUE=Embryo {ECO:0000269|PubMed:8625848};
PubMed=8625848;
Bornemann D., Miller E., Simon J.A.;
"The Drosophila polycomb group gene Sex comb on midleg (Scm) encodes a
zinc finger protein with similarity to polyhomeotic protein.";
Development 122:1621-1630(1996).
[2] {ECO:0000312|EMBL:AAF54419.2}
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=Berkeley {ECO:0000269|PubMed:10731132};
PubMed=10731132; DOI=10.1126/science.287.5461.2185;
Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D.,
Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F.,
George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N.,
Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X.,
Brandon R.C., Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D.,
Wan K.H., Doyle C., Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G.,
Abril J.F., Agbayani A., An H.-J., Andrews-Pfannkoch C., Baldwin D.,
Ballew R.M., Basu A., Baxendale J., Bayraktaroglu L., Beasley E.M.,
Beeson K.Y., Benos P.V., Berman B.P., Bhandari D., Bolshakov S.,
Borkova D., Botchan M.R., Bouck J., Brokstein P., Brottier P.,
Burtis K.C., Busam D.A., Butler H., Cadieu E., Center A., Chandra I.,
Cherry J.M., Cawley S., Dahlke C., Davenport L.B., Davies P.,
de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I., Dietz S.M.,
Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C., Dunn P.,
Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S., Fleischmann W.,
Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M., Glasser K.,
Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M.,
Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J.,
Hostin D., Houston K.A., Howland T.J., Wei M.-H., Ibegwam C.,
Jalali M., Kalush F., Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A.,
Kimmel B.E., Kodira C.D., Kraft C.L., Kravitz S., Kulp D., Lai Z.,
Lasko P., Lei Y., Levitsky A.A., Li J.H., Li Z., Liang Y., Lin X.,
Liu X., Mattei B., McIntosh T.C., McLeod M.P., McPherson D.,
Merkulov G., Milshina N.V., Mobarry C., Morris J., Moshrefi A.,
Mount S.M., Moy M., Murphy B., Murphy L., Muzny D.M., Nelson D.L.,
Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R., Pacleb J.M.,
Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V., Reese M.G.,
Reinert K., Remington K., Saunders R.D.C., Scheeler F., Shen H.,
Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J.,
Spier E., Spradling A.C., Stapleton M., Strong R., Sun E.,
Svirskas R., Tector C., Turner R., Venter E., Wang A.H., Wang X.,
Wang Z.-Y., Wassarman D.A., Weinstock G.M., Weissenbach J.,
Williams S.M., Woodage T., Worley K.C., Wu D., Yang S., Yao Q.A.,
Ye J., Yeh R.-F., Zaveri J.S., Zhan M., Zhang G., Zhao Q., Zheng L.,
Zheng X.H., Zhong F.N., Zhong W., Zhou X., Zhu S.C., Zhu X.,
Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M., Venter J.C.;
"The genome sequence of Drosophila melanogaster.";
Science 287:2185-2195(2000).
[3] {ECO:0000305, ECO:0000312|EMBL:AAF54419.2}
GENOME REANNOTATION.
STRAIN=Berkeley;
PubMed=12537572; DOI=10.1186/gb-2002-3-12-research0083;
Misra S., Crosby M.A., Mungall C.J., Matthews B.B., Campbell K.S.,
Hradecky P., Huang Y., Kaminker J.S., Millburn G.H., Prochnik S.E.,
Smith C.D., Tupy J.L., Whitfield E.J., Bayraktaroglu L., Berman B.P.,
Bettencourt B.R., Celniker S.E., de Grey A.D.N.J., Drysdale R.A.,
Harris N.L., Richter J., Russo S., Schroeder A.J., Shu S.Q.,
Stapleton M., Yamada C., Ashburner M., Gelbart W.M., Rubin G.M.,
Lewis S.E.;
"Annotation of the Drosophila melanogaster euchromatic genome: a
systematic review.";
Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002).
[4] {ECO:0000305, ECO:0000312|EMBL:AAN71320.1}
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=Berkeley {ECO:0000312|EMBL:AAN71320.1};
TISSUE=Embryo {ECO:0000269|PubMed:12537569};
PubMed=12537569; DOI=10.1186/gb-2002-3-12-research0080;
Stapleton M., Carlson J.W., Brokstein P., Yu C., Champe M.,
George R.A., Guarin H., Kronmiller B., Pacleb J.M., Park S., Wan K.H.,
Rubin G.M., Celniker S.E.;
"A Drosophila full-length cDNA resource.";
Genome Biol. 3:RESEARCH0080.1-RESEARCH0080.8(2002).
[5] {ECO:0000305}
INTERACTION WITH PH-P, AND MUTAGENESIS OF ILE-834; GLY-836;
840-LEU-LEU-841 AND LYS-854.
PubMed=9343432; DOI=10.1128/MCB.17.11.6683;
Peterson A.J., Kyba M., Bornemann D., Morgan K., Brock H.W.,
Simon J.A.;
"A domain shared by the polycomb group proteins Scm and ph mediates
heterotypic and homotypic interactions.";
Mol. Cell. Biol. 17:6683-6692(1997).
[6] {ECO:0000305}
INTERACTION WITH CORTO.
PubMed=12771214; DOI=10.1093/nar/gkg381;
Salvaing J., Lopez A., Boivin A., Deutsch J.S., Peronnet F.;
"The Drosophila Corto protein interacts with Polycomb-group proteins
and the GAGA factor.";
Nucleic Acids Res. 31:2873-2882(2003).
[7] {ECO:0000305}
FUNCTION, ASSOCIATION WITH PRC1 COMPLEX, AND MUTAGENESIS OF GLU-816;
GLY-836; MET-846; MET-848; MET-851 AND LYS-860.
PubMed=15280237; DOI=10.1534/genetics.104.027474;
Peterson A.J., Mallin D.R., Francis N.J., Ketel C.S., Stamm J.,
Voeller R.K., Kingston R.E., Simon J.A.;
"Requirement for sex comb on midleg protein interactions in Drosophila
polycomb group repression.";
Genetics 167:1225-1239(2004).
[8]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-546; SER-549; SER-550
AND SER-585, AND IDENTIFICATION BY MASS SPECTROMETRY.
TISSUE=Embryo;
PubMed=18327897; DOI=10.1021/pr700696a;
Zhai B., Villen J., Beausoleil S.A., Mintseris J., Gygi S.P.;
"Phosphoproteome analysis of Drosophila melanogaster embryos.";
J. Proteome Res. 7:1675-1682(2008).
[9] {ECO:0000305}
X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 795-871, AND INTERACTION WITH
PH-P.
PubMed=15905166; DOI=10.1074/jbc.M503055200;
Kim C.A., Sawaya M.R., Cascio D., Kim W., Bowie J.U.;
"Structural organization of a Sex-comb-on-midleg/polyhomeotic
copolymer.";
J. Biol. Chem. 280:27769-27775(2005).
-!- FUNCTION: Polycomb group (PcG) protein. PcG proteins act by
forming multiprotein complexes, which are required to maintain the
transcriptionally repressive state of homeotic genes throughout
development. PcG proteins are not required to initiate repression,
but to maintain it during later stages of development. They
probably act via the methylation of histones, rendering chromatin
heritably changed in its expressibility.
{ECO:0000250|UniProtKB:Q9W3C1, ECO:0000269|PubMed:15280237}.
-!- SUBUNIT: Scm associates with the PRC1 core complex containing PSC,
PC, PH and Sce/RING1. Forms homotypic and heterotypic
interactions. Interacts with the SAM domain of ph-p via its SAM
domain in vitro. Interacts with corto in vitro.
{ECO:0000269|PubMed:12771214, ECO:0000269|PubMed:15280237,
ECO:0000269|PubMed:15905166, ECO:0000269|PubMed:9343432}.
-!- INTERACTION:
Self; NbExp=4; IntAct=EBI-89256, EBI-89256;
P41046:corto; NbExp=2; IntAct=EBI-89256, EBI-300379;
P02299:His3:CG33854; NbExp=4; IntAct=EBI-89256, EBI-522090;
P39769:ph-p; NbExp=6; IntAct=EBI-89256, EBI-300360;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
-!- DEVELOPMENTAL STAGE: Expressed both maternally and zygotically.
Levels are highest in 0-2 hours embryos and at lower levels during
later embryonic and larval stages. A modest increase in expression
is seen during the pupal stage. Expressed throughout the 9 hours
embryo. After 12 hours expression is concentrated in the central
nervous system. {ECO:0000269|PubMed:8625848}.
-!- DOMAIN: The SAM domain is essential for function.
{ECO:0000269|PubMed:15280237}.
-!- SIMILARITY: Belongs to the SCM family. {ECO:0000255}.
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EMBL; U49793; AAB57632.1; -; mRNA.
EMBL; AE014297; AAF54419.2; -; Genomic_DNA.
EMBL; BT001565; AAN71320.1; -; mRNA.
RefSeq; NP_001247006.1; NM_001260077.2.
RefSeq; NP_731385.1; NM_169299.2.
UniGene; Dm.6241; -.
PDB; 1PK1; X-ray; 1.80 A; B/D=795-871.
PDB; 1PK3; X-ray; 1.85 A; A/B/C=795-871.
PDB; 2R57; X-ray; 2.20 A; A=175-435.
PDB; 2R58; X-ray; 2.00 A; A=175-435.
PDB; 2R5A; X-ray; 2.30 A; A=175-435.
PDB; 2R5M; X-ray; 2.65 A; A=175-435.
PDB; 5J8Y; X-ray; 1.98 A; A/B=803-877.
PDBsum; 1PK1; -.
PDBsum; 1PK3; -.
PDBsum; 2R57; -.
PDBsum; 2R58; -.
PDBsum; 2R5A; -.
PDBsum; 2R5M; -.
PDBsum; 5J8Y; -.
ProteinModelPortal; Q9VHA0; -.
SMR; Q9VHA0; -.
BioGrid; 66327; 43.
DIP; DIP-17570N; -.
IntAct; Q9VHA0; 9.
MINT; MINT-266904; -.
STRING; 7227.FBpp0081580; -.
iPTMnet; Q9VHA0; -.
PaxDb; Q9VHA0; -.
PRIDE; Q9VHA0; -.
EnsemblMetazoa; FBtr0082102; FBpp0081580; FBgn0003334.
EnsemblMetazoa; FBtr0306008; FBpp0297150; FBgn0003334.
GeneID; 41168; -.
KEGG; dme:Dmel_CG9495; -.
CTD; 41168; -.
FlyBase; FBgn0003334; Scm.
eggNOG; ENOG410IMEZ; Eukaryota.
eggNOG; ENOG410XPKI; LUCA.
GeneTree; ENSGT00760000119024; -.
InParanoid; Q9VHA0; -.
KO; K11461; -.
OMA; KILNNAM; -.
OrthoDB; EOG091G05BW; -.
PhylomeDB; Q9VHA0; -.
Reactome; R-DME-2559580; Oxidative Stress Induced Senescence.
Reactome; R-DME-3108214; SUMOylation of DNA damage response and repair proteins.
Reactome; R-DME-4570464; SUMOylation of RNA binding proteins.
EvolutionaryTrace; Q9VHA0; -.
GenomeRNAi; 41168; -.
PRO; PR:Q9VHA0; -.
Proteomes; UP000000803; Chromosome 3R.
Bgee; FBgn0003334; -.
ExpressionAtlas; Q9VHA0; differential.
Genevisible; Q9VHA0; DM.
GO; GO:0005634; C:nucleus; IDA:FlyBase.
GO; GO:0005700; C:polytene chromosome; IDA:FlyBase.
GO; GO:0035102; C:PRC1 complex; TAS:FlyBase.
GO; GO:0042802; F:identical protein binding; IPI:UniProtKB.
GO; GO:0008270; F:zinc ion binding; NAS:UniProtKB.
GO; GO:0007409; P:axonogenesis; IMP:FlyBase.
GO; GO:0048749; P:compound eye development; IMP:FlyBase.
GO; GO:0016569; P:covalent chromatin modification; IEA:UniProtKB-KW.
GO; GO:0016458; P:gene silencing; IMP:UniProtKB.
GO; GO:0030708; P:germarium-derived female germ-line cyst encapsulation; IMP:FlyBase.
GO; GO:0045926; P:negative regulation of growth; IMP:FlyBase.
GO; GO:0045892; P:negative regulation of transcription, DNA-templated; TAS:UniProtKB.
GO; GO:0022008; P:neurogenesis; IMP:FlyBase.
GO; GO:0030713; P:ovarian follicle cell stalk formation; IMP:FlyBase.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
GO; GO:0007419; P:ventral cord development; IMP:FlyBase.
InterPro; IPR004092; Mbt.
InterPro; IPR001660; SAM.
InterPro; IPR013761; SAM/pointed.
InterPro; IPR021987; SLED.
InterPro; IPR012313; Znf_FCS.
InterPro; IPR010507; Znf_MYM.
Pfam; PF02820; MBT; 2.
Pfam; PF00536; SAM_1; 1.
Pfam; PF12140; SLED; 1.
Pfam; PF06467; zf-FCS; 1.
SMART; SM00561; MBT; 2.
SMART; SM00454; SAM; 1.
SUPFAM; SSF47769; SSF47769; 1.
PROSITE; PS51079; MBT; 2.
PROSITE; PS50105; SAM_DOMAIN; 1.
PROSITE; PS51024; ZF_FCS; 1.
1: Evidence at protein level;
3D-structure; Chromatin regulator; Complete proteome;
Developmental protein; Metal-binding; Nucleus; Phosphoprotein;
Reference proteome; Repeat; Repressor; Transcription;
Transcription regulation; Zinc; Zinc-finger.
CHAIN 1 877 Polycomb protein Scm.
/FTId=PRO_0000114333.
REPEAT 175 273 MBT 1. {ECO:0000255}.
REPEAT 281 382 MBT 2. {ECO:0000255}.
DOMAIN 806 876 SAM. {ECO:0000255|PROSITE-
ProRule:PRU00184}.
ZN_FING 54 93 FCS-type. {ECO:0000255|PROSITE-
ProRule:PRU00367}.
COMPBIAS 7 49 Ser-rich. {ECO:0000255}.
COMPBIAS 672 750 Ser-rich. {ECO:0000255}.
COMPBIAS 751 776 Ala-rich. {ECO:0000255}.
MOD_RES 546 546 Phosphothreonine.
{ECO:0000269|PubMed:18327897}.
MOD_RES 549 549 Phosphoserine.
{ECO:0000269|PubMed:18327897}.
MOD_RES 550 550 Phosphoserine.
{ECO:0000269|PubMed:18327897}.
MOD_RES 585 585 Phosphoserine.
{ECO:0000269|PubMed:18327897}.
MUTAGEN 816 816 E->G: No effect on function. Shows
self- and ph-p binding activity
comparable to wild-type; when associated
with V-846 and R-860.
{ECO:0000269|PubMed:15280237}.
MUTAGEN 834 834 I->T: Complete loss of function.
Significant loss of self-binding
activity. Moderate loss of ph-p binding
activity. {ECO:0000269|PubMed:9343432}.
MUTAGEN 836 836 G->D: Complete loss of function. Complete
loss of self- and ph-p binding activity.
{ECO:0000269|PubMed:15280237,
ECO:0000269|PubMed:9343432}.
MUTAGEN 836 836 G->S: Loss of self- and ph-p binding
activity. {ECO:0000269|PubMed:15280237,
ECO:0000269|PubMed:9343432}.
MUTAGEN 840 841 LL->SS: Several-fold reduction of self-
binding activity. Partial loss of ph-p
binding activity.
{ECO:0000269|PubMed:9343432}.
MUTAGEN 846 846 M->V: No effect on function. Shows
self- and ph-p binding activity
comparable to wild-type; when associated
with G-816 and R-860.
{ECO:0000269|PubMed:15280237}.
MUTAGEN 848 848 Missing: Complete loss of function.
Significant loss of self-binding
activity. Partial loss of ph-p binding
activity. {ECO:0000269|PubMed:15280237}.
MUTAGEN 851 851 M->R: Complete loss of function. Complete
loss of self- and ph-p binding activity.
{ECO:0000269|PubMed:15280237}.
MUTAGEN 854 854 K->A: Partial loss of self- and ph-p
binding activity.
{ECO:0000269|PubMed:9343432}.
MUTAGEN 860 860 K->E: Complete loss of function. Partial
loss of self-binding activity. Complete
loss of ph-p binding activity.
{ECO:0000269|PubMed:15280237}.
MUTAGEN 860 860 K->R: No effect on function. Shows
self- and ph-p binding activity
comparable to wild-type; when associated
with G-816 and V-846.
{ECO:0000269|PubMed:15280237}.
HELIX 177 183 {ECO:0000244|PDB:2R58}.
HELIX 191 193 {ECO:0000244|PDB:2R58}.
STRAND 194 196 {ECO:0000244|PDB:2R58}.
STRAND 210 215 {ECO:0000244|PDB:2R58}.
STRAND 218 231 {ECO:0000244|PDB:2R58}.
STRAND 234 239 {ECO:0000244|PDB:2R58}.
STRAND 248 251 {ECO:0000244|PDB:2R58}.
HELIX 262 265 {ECO:0000244|PDB:2R58}.
HELIX 280 282 {ECO:0000244|PDB:2R58}.
HELIX 283 291 {ECO:0000244|PDB:2R58}.
HELIX 299 301 {ECO:0000244|PDB:2R58}.
STRAND 319 323 {ECO:0000244|PDB:2R58}.
STRAND 331 340 {ECO:0000244|PDB:2R58}.
STRAND 343 348 {ECO:0000244|PDB:2R58}.
HELIX 353 355 {ECO:0000244|PDB:2R58}.
STRAND 357 360 {ECO:0000244|PDB:2R58}.
HELIX 371 375 {ECO:0000244|PDB:2R58}.
HELIX 797 800 {ECO:0000244|PDB:1PK3}.
HELIX 803 805 {ECO:0000244|PDB:1PK1}.
HELIX 808 818 {ECO:0000244|PDB:1PK1}.
HELIX 820 825 {ECO:0000244|PDB:1PK1}.
HELIX 826 831 {ECO:0000244|PDB:1PK1}.
HELIX 836 840 {ECO:0000244|PDB:1PK1}.
HELIX 844 850 {ECO:0000244|PDB:1PK1}.
HELIX 855 868 {ECO:0000244|PDB:1PK1}.
SEQUENCE 877 AA; 93551 MW; 7859FD0C7B91589E CRC64;
MSGGRDSSTS SGSNSAAPGA STNATSSASA SASSTSTSAS PGSTTSPAST QRQRGRPAKR
ATCTWCGEGK LPLQYVLPTQ TGKKEFCSET CIAEFRKAYS KGACTQCDNV IRDGAPNKEF
CSIMCMNKHQ KKNCSTRHSG GSASGKGLAE SERKLLASGA PAPTGPFQYE SFHVFDWDAY
LEETGSEAAP AKCFKQAQNP PNNDFKIGMK LEALDPRNVT STCIATVVGV LGSRLRLRLD
GSDSQNDFWR LVDSTEIHAI GHCEKNGGML QPPLGFRMNA SSWPGYLCKI LNNAMVAPEE
IFQPEPPEPE ENLFKVGQKL EAVDKKNPQL ICCATVDAIK DDQIHVTFDG WRGAFDYWCN
YRSRDIFPAG WCARSCHPMQ PPGHKSRMDS SSSKQRCPRP RYTVVAESEA MVPASPATAH
FHPNCKGGPF INNSKLPCMV TGPTYQTLAK LCLQEVLAAS TDTQQLSKLL FALEGDVHIV
TAAGKNFTVK IPSPMRMKDD ESLAQFIETL CTTCRACANL ISLVHETEEC KKCANSRKRQ
LTQSATPPSS PVLADKRNRQ SNSATTSPSE KIIKQELAVK SPVESKSKTS TNNGKEPASQ
QNSNHSLNNN NNSASKSSNK VVIKSEPNGA NAQTSSTTQA LRKVRFQHHA NTNTNSSATN
GNQDTSQTTH VSTSHCSSSS TSSSTSLAGG SANTSTIGKY LAPLVAEVHP EQANVKPSNS
YYKSPTTLSS SASLPTSVST PFTGCQSASS TALAAGGVTA AKAATAPAGA AATAGASPSY
TAITSPVSTP TSALANSHLR SQPIDWTIEE VIQYIESNDN SLAVHGDLFR KHEIDGKALL
LLNSEMMMKY MGLKLGPALK ICNLVNKVNG RRNNLAL


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